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Bacterial whole genome sequencing

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https://www.readbyqxmd.com/read/29040419/high-rates-of-human-fecal-carriage-of-mcr-1-positive-multi-drug-resistant-enterobacteriaceae-isolates-emerge-in-china-in-association-with-successful-plasmid-families
#1
Lan-Lan Zhong, Hang T T Phan, Cong Shen, Karina Doris-Vihta, Anna E Sheppard, Xi Huang, Kun-Jiao Zeng, Hong-Yu Li, Xue-Fei Zhang, Sandip Patil, Derrick W Crook, A Sarah Walker, Yong Xing, Jia-Lin Lin, Lian-Qiang Feng, Yohei Doi, Yong Xia, Nicole Stoesser, Guo-Bao Tian
Objectives: mcr-1-mediated colistin resistance in Enterobacteriaceae is concerning, as colistin is used in treating multidrug-resistant Enterobacteriaceae infections. Rates of human mcr-1 gastrointestinal carriage have historically been low. We identified trends in human fecal mcr-1-positivity rates and colonization with mcr-1-positive+third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae in Guangzhou, China, and investigated the genetic contexts of mcr-1 in a subset of mcr-1-positive+3GC-R strains...
October 10, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29036291/phylotyper-in-silico-predictor-of-gene-subtypes
#2
Matthew D Whiteside, Victor P J Gannon, Chad R Laing
Summary: Whole genome sequencing (WGS) is being adopted in public health for improved surveillance and outbreak analysis. In public health, subtyping has been used to infer phenotypes and distinguish bacterial strain groups. In silico tools that predict subtypes from sequences data are needed to transition historical data to WGS-based protocols. Phylotyper is a novel solution for in silico subtype prediction from gene sequences. Designed for incorporation into WGS pipelines, it is a general prediction tool that can be applied to different subtype schemes...
July 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29034633/-comparison-of-effects-of-staphylococcal-nuclease-a-fused-with-different-exogenous-dna-fragments
#3
Lixia Fu, Dejun Ji, Xubin Lu, Xian'gan Han, Wenzhi Wei
Staphylococcal nuclease A (SNA) may be used to produce bacterial ghosts for further inactivation of host bacteria and elimination of residual genetic materials. It is still controversial if SNA without signal peptide can be secreted to extracellular matrix and if fusion with other peptide is required for its function in the cytoplasm of host bacteria. To clarify this dispute, a series of temperature-inducible plasmids carrying SNA alone or SNA fused with partial sequences of λ phage cro gene (cSNA) or Mycobacterium tuberculosis urease gene (uSNA) were constructed and evaluated in Escherichia coli...
December 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29028989/phast-phaster-and-phastest-tools-for-finding-prophage-in-bacterial-genomes
#4
David Arndt, Ana Marcu, Yongjie Liang, David S Wishart
PHAST (PHAge Search Tool) and its successor PHASTER (PHAge Search Tool - Enhanced Release) have become two of the most widely used web servers for identifying putative prophages in bacterial genomes. Here we review the main capabilities of these web resources, provide some practical guidance regarding their use and discuss possible future improvements. PHAST, which was first described in 2011, made its debut just as whole bacterial genome sequencing and was becoming inexpensive and relatively routine. PHAST quickly gained popularity among bacterial genome researchers because of its web accessibility, its ease of use along with its enhanced accuracy and rapid processing times...
September 25, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29026654/population-genetic-structuring-of-methicillin-resistant-staphylococcus-aureus-clone-emrsa-15-within-uk-reflects-patient-referral-patterns
#5
Tjibbe Donker, Sandra Reuter, James Scriberras, Rosy Reynolds, Nicholas M Brown, M Estée Török, Richard James, East Of England Microbiology Research Network, David M Aanensen, Stephen D Bentley, Matthew T G Holden, Julian Parkhill, Brian G Spratt, Sharon J Peacock, Edward J Feil, Hajo Grundmann
Antibiotic resistance forms a serious threat to the health of hospitalised patients, rendering otherwise treatable bacterial infections potentially life-threatening. A thorough understanding of the mechanisms by which resistance spreads between patients in different hospitals is required in order to design effective control strategies. We measured the differences between bacterial populations of 52 hospitals in the United Kingdom and Ireland, using whole-genome sequences from 1085 MRSA clonal complex 22 isolates collected between 1998 and 2012...
July 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29024922/isolation-and-whole-genome-analysis-of-endospore-forming-bacteria-from-heroin
#6
Jörn Kalinowski, Björn Ahrens, Arwa Al-Dilaimi, Anika Winkler, Daniel Wibberg, Uwe Schleenbecker, Christian Rückert, Roman Wölfel, Gregor Grass
Infections caused by endospore-forming bacteria have been associated with severe illness and death among persons who inject drugs. Analysis of the bacteria residing in heroin has thus been biased towards species that affect human health. Similarly, exploration of the bacterial diversity of seized street market heroin correlated with the skin microflora of recreational heroin users insofar as different Staphylococus spp. or typical environmental endospore formers including Bacillus cereus and other Bacilli outside the B...
October 4, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29018124/straight-from-the-horse-s-mouth-genomic-epidemiology-of-an-icelandic-equine-epidemic
#7
Mark R Davies
Despite tight biosecurity measures, an outbreak of respiratory disease rapidly spread across the Icelandic equine population in 2010. Horse transportation was brought to a halt in order to contain the spread of the infectious agent. In a recent article, Björnsdóttir and colleagues (S. Björnsdóttir et al., mBio 8:e00826-17, 2017, https://doi.org/10.1128/mBio.00826-17) employ the power and resolution of "genomic epidemiology," the combination of whole genomic sequencing and epidemiological approaches, to examine the source and spread of the outbreak...
October 10, 2017: MBio
https://www.readbyqxmd.com/read/29017452/whole-genome-sequencing-for-the-molecular-characterization-of-carbapenem-resistant-klebsiella-pneumoniae-strains-isolated-at-the-italian-asst-fatebenefratelli-sacco-hospital-2012-2014
#8
Sara Giordana Rimoldi, Bernardina Gentile, Cristina Pagani, Annamaria Di Gregorio, Anna Anselmo, Anna Maria Palozzi, Antonella Fortunato, Valentina Pittiglio, Anna Lisa Ridolfo, Maria Rita Gismondo, Giuliano Rizzardini, Florigio Lista
BACKGROUND: The emergence of carbapenem-resistant Klebsiella pneumoniae strains is threatening antimicrobial treatment. METHODS: Sixty-eight carbapenemase-producing K. pneumoniae strains isolated at Luigi Sacco University Hospital-ASST Fatebenefratelli Sacco (Milan, Italy) between 2012 and 2014 were characterised microbiologically and molecularly. They were tested for drug susceptibility and carbapenemase phenotypes, investigated by means of repetitive extra-genic palindromic polymerase chain reaction (REP-PCR), and fully sequenced by means of next-generation sequencing for the in silico analysis of multi-locus sequence typing (MLST), their resistome, virulome and plasmid content, and their core single nucleotide polymorphism (SNP) genotypes...
October 10, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28993337/whole-transcriptome-and-genomic-analysis-of-extensively-drug-resistant-mycobacterium-tuberculosis-clinical-isolates-identifies-downregulation-of-etha-as-a-mechanism-of-ethionamide-resistance
#9
Lynne de Welzen, Vegard Eldholm, Kashmeel Maharaj, Abigail L Manson, Ashlee M Earl, Alexander S Pym
Genetic based drug susceptibility testing has improved the diagnosis of drug-resistant tuberculosis, but is limited by our lack of knowledge of all resistance mechanisms. Next generation sequencing has assisted in identifying the principal genetic mechanisms of resistance for many drugs, but a significant proportion of phenotypic drug resistance is unexplained genetically. Few studies have formally compared the transcriptome of susceptible and resistant M. tuberculosis We carried out comparative whole genome transcriptomics on extensively drug-resistant (XDR) clinical isolates using RNA-sequencing (RNAseq) to find novel transcriptional mediated mechanisms of resistance...
October 9, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28989277/a-metagenomic-analysis-of-bacterial-microbiota-in-the-digestive-tract-of-triatomines
#10
Nicolas Carels, Marcial Gumiel, Fabio Faria da Mota, Carlos José de Carvalho Moreira, Patricia Azambuja
The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. The enzymatic reactions encoded by coding sequences of both rare and common bacterial species were then compared and revealed key functions explaining why some genera outcompete others in the DTT...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28987590/viable-mycobacterium-avium-ssp-paratuberculosis-isolated-from-calf-milk-replacer
#11
Irene R Grant, Antonio C G Foddai, James C Tarrant, Brenna Kunkel, Faye A Hartmann, Sheila McGuirk, Chungyi Hansen, Adel M Talaat, Michael T Collins
When advising farmers on how to control Johne's disease in an infected herd, one of the main recommendations is to avoid feeding waste milk to calves and instead feed calf milk replacer (CMR). This advice is based on the assumption that CMR is free of viable Mycobacterium avium ssp. paratuberculosis (MAP) cells, an assumption that has not previously been challenged. We tested commercial CMR products (n = 83) obtained from dairy farms around the United States by the peptide-mediated magnetic separation (PMS)-phage assay, PMS followed by liquid culture (PMS-culture), and direct IS900 quantitative PCR (qPCR)...
October 4, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28981392/extended-spectrum-beta-lactamase-ampc-beta-lactamase-producing-enterobacteriaceae-in-broiler-farms-transmission-dynamics-at-farm-level
#12
Katrin Daehre, Michaela Projahn, Torsten Semmler, Uwe Roesler, Anika Friese
The occurrence of extended-spectrum beta-lactamase- (ESBL) and/or AmpC beta-lactamase- (AmpC) producing Enterobacteriaceae in livestock, especially in broiler fattening flocks, has been demonstrated in previous studies. Nevertheless, data on transmission routes of these resistant bacteria into the fattening farms are rare. Therefore, seven broiler fattening flocks were investigated for the occurrence of ESBL-/AmpC-producing Enterobacteriaceae during the course of the fattening period with the special focus on horizontal transmission routes...
October 5, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28962627/laboratory-acquired-infections-of-salmonella-enterica-serotype-typhi-in-south-africa-phenotypic-and-genotypic-analysis-of-isolates
#13
Anthony Marius Smith, Shannon Lucrecia Smouse, Nomsa Pauline Tau, Colleen Bamford, Vineshree Mischka Moodley, Charlene Jacobs, Kerrigan Mary McCarthy, Adré Lourens, Karen Helena Keddy
BACKGROUND: Workers in clinical microbiology laboratories are exposed to a variety of pathogenic microorganisms. Salmonella species is among the most commonly reported bacterial causes of laboratory-acquired infections. We report on three cases of laboratory-acquired Salmonella enterica serotype Typhi (Salmonella Typhi) infection which occurred over the period 2012 to 2016 in South Africa. METHODS: Laboratory investigation included phenotypic and genotypic characterization of isolates...
September 29, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28959742/the-biofilm-inhibitor-carolacton-enters-gram-negative-cells-studies-using-a-tolc-deficient-strain-of-escherichia-coli
#14
Jannik Donner, Michael Reck, Boyke Bunk, Michael Jarek, Constantin Benjamin App, Jan P Meier-Kolthoff, Jörg Overmann, Rolf Müller, Andreas Kirschning, Irene Wagner-Döbler
The myxobacterial secondary metabolite carolacton inhibits growth of Streptococcus pneumoniae and kills biofilm cells of the caries- and endocarditis-associated pathogen Streptococcus mutans at nanomolar concentrations. Here, we studied the response to carolacton of an Escherichia coli strain that lacked the outer membrane protein TolC. Whole-genome sequencing of the laboratory E. coli strain TolC revealed the integration of an insertion element, IS5, at the tolC locus and a close phylogenetic relationship to the ancient E...
September 2017: MSphere
https://www.readbyqxmd.com/read/28955357/comparative-genomics-of-ralstonia-solanacearum-identifies-candidate-genes-associated-with-cool-virulence
#15
Ana M Bocsanczy, Jose C Huguet-Tapia, David J Norman
Strains of the Ralstonia solanacearum species complex in the phylotype IIB group are capable of causing Bacterial Wilt disease in potato and tomato at temperatures lower than 24°C. The capability of these strains to survive and to incite infection at temperatures colder than their normally tropical boundaries represents a threat to United States agriculture in temperate regions. In this work, we used a comparative genomics approach to identify orthologous genes linked to the lower temperature virulence phenotype...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28947104/examination-into-the-taxonomic-position-of-bacillus-thermotolerans-yang-et-al-2013-proposal-for-its-reclassification-into-a-new-genus-and-species-quasibacillus-thermotolerans-gen-nov-comb-nov-and-reclassification-of-b-encimensis-dastager-et-al-2015-as-a-later
#16
Ashish Verma, Yash Pal, Indu Khatri, Anup Kumar Ojha, Harald Gruber-Vodicka, Peter Schumann, Syed Dastager, Srikrishna Subramanian, Shanmugam Mayilraj, Srinivasan Krishnamurthi
Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8(T) confirmed their separation into a novel genus with B...
September 12, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28943151/genomic-characterization-phylogenetic-analysis-and-identification-of-virulence-factors-in-aerococcus-sanguinicola-and-aerococcus-urinae-strains-isolated-from-infection-episodes
#17
Derya Carkaci, Katrine Højholt, Xiaohui Chen Nielsen, Rimtas Dargis, Simon Rasmussen, Ole Skovgaard, Kurt Fuursted, Paal Skytt Andersen, Marc Stegger, Jens Jørgen Christensen
Aerococcus sanguinicola and Aerococcus urinae are emerging pathogens in clinical settings mostly being causative agents of urinary tract infections (UTIs), urogenic sepsis and more seldomly complicated infective endocarditis (IE). Limited knowledge exists concerning the pathogenicity of these two species. Eight clinical A. sanguinicola (isolated from 2009 to 2015) and 40 clinical A. urinae (isolated from 1984 to 2015) strains from episodes of UTIs, bacteremia, and IE were whole-genome sequenced (WGS) to analyze genomic diversity and characterization of virulence genes involved in the bacterial pathogenicity...
September 21, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28937735/whole-genome-shotgun-sequencing-of-two-%C3%AE-proteobacterial-species-in-search-of-the-bulgecin-biosynthetic-cluster
#18
Mark E Horsman, Daniel R Marous, Rongfeng Li, Ryan A Oliver, Byungjin Byun, Scott J Emrich, Bill Boggess, Craig A Townsend, Shahriar Mobashery
We have produced draft whole-genome sequences for two bacterial strains reported to produce the bulgecins as well as NRPS-derived monobactam β-lactam antibiotics. We propose classification of ATCC 31363 as Paraburkholderia acidophila. We further reaffirm that ATCC 31433 (Burkholderia ubonensis subsp. mesacidophila) is a taxonomically distinct producer of bulgecins with notable gene regions shared with Paraburkholderia acidophila. We use RAST multiple-gene comparison and MASH distancing with published genomes to order the draft contigs and identify unique gene regions for characterization...
September 26, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28935481/stalking-a-lethal-superbug-by-whole-genome-sequencing-and-phylogenetics-influence-on-unraveling-a-major-hospital-outbreak-of-carbapenem-resistant-klebsiella-pneumoniae
#19
Thorsten Kaiser, Knut Finstermeier, Madlen Häntzsch, Sarah Faucheux, Martin Kaase, Tim Eckmanns, Sven Bercker, Udo X Kaisers, Norman Lippmann, Arne C Rodloff, Joachim Thiery, Christoph Lübbert
BACKGROUND: From July 2010-April 2013, Leipzig University Hospital experienced the largest outbreak of a Klebsiella pneumoniae carbapenemase 2 (KPC-2)-producing Klebsiella pneumoniae (KPC-2-Kp) strain observed in Germany to date. After termination of the outbreak, we aimed to reconstruct transmission pathways by phylogenetics based on whole-genome sequencing (WGS). METHODS: One hundred seventeen KPC-2-Kp isolates from 89 outbreak patients, 5 environmental KPC-2-Kp isolates, and 24 K pneumoniae strains not linked to the outbreak underwent WGS...
September 18, 2017: American Journal of Infection Control
https://www.readbyqxmd.com/read/28933324/photobacterium-toruni-sp-nov-a-bacterium-isolated-from-diseased-farmed-fish
#20
Alejandro M Labella, David R Arahal, Teresa Lucena, Manuel Manchado, Dolores Castro, Juan J Borrego
Three bacterial strains were isolated from liver and spleen of diseased farmed redbanded seabream (Pagrus auriga) in south-west Spain. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium, showing high similarity (98.6-99.3 %) to the type strains of Photobacterium iliopiscarium, P. piscicola, P. kishitanii, P. aquimaris and P. phosphoreum. Multilocus sequence analysis using six housekeeping genes (gapA, topA, mreB, ftsZ, gyrB and 16S rRNA) confirmed the new strains as forming an independent branch with a bootstrap value of 100, likely to represent a novel species...
September 21, 2017: International Journal of Systematic and Evolutionary Microbiology
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